xyz format
The xyz format is used in computational chemistry and bioinformatics and contains Cartesian coordinates in three dimensions to describe the positions of atoms in molecules . The unit of measurement used is mostly Ångström , less often atomic units .
This format is understood by many programs, but a formal definition has never been published. Therefore, the format can differ slightly depending on the computer program used, or the respective program can have problems reading non-compliant xyz files.
Format specification
Like most of the file formats used in computer chemistry, the xyz format has a line-oriented structure:
1. Zeile: Anzahl der Atome (Ganzzahl) 2. Zeile: Kommentar (Zeichenkette) 3. Zeile und folgende: Elementname x- y- z-Koordinaten (Zeichenkette bzw. Ganzzahl, 3 Kommazahlen)
In its most general variant, the xyz format allows the specification of one (atomic charge, decimal point), three (Cartesian oscillation vector, 3 decimal numbers) or four (oscillation vector and atomic charge) additional columns in the atomic specifications from the third line.
Element x y z [x-vektor y-vektor z-vektor] [q]
Unlike other widely used file formats (e.g. pdb format ), the xyz format does not specify any fixed number formats and positions.
example
An example file for the water molecule is shown below. All coordinates (from line 3, columns 2 to 4) are given in Ångström, the charges as multiples of the elementary charge:
3
Wassermolekül, in x-y-Ebene liegend; AM1-Rechnung
O 0.000000 0.000000 0.000000 -0.382710
H 0.961151 0.000000 0.000000 0.191355
H -0.224986 0.934448 0.000000 0.191355